Qploidy

MaRDI QIDQ7375206CRANFDO

Authors Cristiane Taniguti

Last update 11 July 2026

Copyright license Affero General Public License

Software version identifier PACKAGES.rds, 1.0.1, 1.5.4

Description

Provides functions for estimating ploidy levels and detecting aneuploidy in individuals using allele intensities or allele count data from high-throughput genotyping platforms, including single nucleotide polymorphism (SNP) arrays and sequencing-based technologies. Implements method described in Taniguti et al. (2025) <doi:10.1002/tpg2.70044> an extended version of the 'PennCNV' signal standardization method by Wang et al. (2007) <doi:10.1101/gr.6861907> for higher ploidy levels. Computes B-allele frequencies (BAF), z-scores, and identifies copy number variation patterns.

Cites work

• Exploring chromosomal variations in garden roses: Insights from high‐density SNP array data and a new tool, Qploidy
• PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data

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